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Wang Q, Kline EC, Gilligan-Steinberg SD, Lai JJ, Hull IT, Olanrewaju AO, Panpradist N, Lutz BR. Sensitive Pathogen Detection and Drug Resistance Characterization Using Pathogen-Derived Enzyme Activity Amplified by LAMP or CRISPR-Cas. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.29.24305085. [PMID: 38633802 PMCID: PMC11023665 DOI: 10.1101/2024.03.29.24305085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Pathogens encapsulate or encode their own suite of enzymes to facilitate replication in the host. The pathogen-derived enzymes possess specialized activities that are essential for pathogen replication and have naturally been candidates for drug targets. Phenotypic assays detecting the activities of pathogen-derived enzymes and characterizing their inhibition under drugs offer an opportunity for pathogen detection, drug resistance testing for individual patients, and as a research tool for new drug development. Here, we used HIV as an example to develop assays targeting the reverse transcriptase (RT) enzyme encapsulated in HIV for sensitive detection and phenotypic characterization, with the potential for point-of-care (POC) applications. Specifically, we targeted the complementary (cDNA) generation activity of the HIV RT enzyme by adding engineered RNA as substrates for HIV RT enzyme to generate cDNA products, followed by cDNA amplification and detection facilitated by loop-mediated isothermal amplification (LAMP) or CRISPR-Cas systems. To guide the assay design, we first used qPCR to characterize the cDNA generation activity of HIV RT enzyme. In the LAMP-mediated Product-Amplified RT activity assay (LamPART), the cDNA generation and LAMP amplification were combined into one pot with novel assay designs. When coupled with direct immunocapture of HIV RT enzyme for sample preparation and endpoint lateral flow assays for detection, LamPART detected as few as 20 copies of HIV RT enzyme spiked into 25μL plasma (fingerstick volume), equivalent to a single virion. In the Cas-mediated Product-Amplified RT activity assay (CasPART), we tailored the substrate design to achieve a LoD of 2e4 copies (1.67fM) of HIV RT enzyme. Furthermore, with its phenotypic characterization capability, CasPART was used to characterize the inhibition of HIV RT enzyme under antiretroviral drugs and differentiate between wild-type and mutant HIV RT enzyme for potential phenotypic drug resistance testing. Moreover, the CasPART assay can be readily adapted to target the activity of other pathogen-derived enzymes. As a proof-of-concept, we successfully adapted CasPART to detect HIV integrase with a sensitivity of 83nM. We anticipate the developed approach of detecting enzyme activity with product amplification has the potential for a wide range of pathogen detection and phenotypic characterization.
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Affiliation(s)
- Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ayokunle O. Olanrewaju
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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2
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Jiang KP, Bennett S, Heiniger EK, Kumar S, Yager P. UbiNAAT: a multiplexed point-of-care nucleic acid diagnostic platform for rapid at-home pathogen detection. LAB ON A CHIP 2024; 24:492-504. [PMID: 38164805 DOI: 10.1039/d3lc00753g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The COVID-19 pandemic increased demands for respiratory disease testing to facilitate treatment and limit transmission, demonstrating in the process that most existing test options were too complex and expensive to perform in point-of-care or home scenarios. Lab-based molecular techniques can detect viral RNA in respiratory illnesses but are expensive and require trained personnel, while affordable antigen-based home tests lack sensitivity for early detection in newly infected or asymptomatic individuals. The few home RNA detection tests deployed were prohibitively expensive. Here, we demonstrate a point-of-care, paper-based rapid analysis device that simultaneously detects multiple viral RNAs; it is demonstrated on two common respiratory viruses (COVID-19 and influenza A) spiked onto a commercial nasal swab. The automated device requires no sample preparation by the user after insertion of the swab, minimizing user operation steps. We incorporated lyophilized amplification reagents immobilized in a porous matrix, a novel thermally actuated valve for multiplexed fluidic control, a printed circuit board that performs on-device lysis and amplification within a cell-phone-sized disposable device. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized via fluorescent dyes using a modified cell phone, resulting in detection of as few as 104 viral copies per swab across both pathogens within 30 minutes. This integrated platform could be commercialized in a form that would be inexpensive, portable, and sensitive; it can readily be multiplexed to detect as many as 8 different RNA or DNA sequences, and adapted to any desired RNA or DNA detection assays.
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Affiliation(s)
- Kevin P Jiang
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Steven Bennett
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Erin K Heiniger
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Sujatha Kumar
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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3
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an integrated sample amplification control for salivary point-of-care pathogen testing. Anal Chim Acta 2024; 1287:342072. [PMID: 38182338 DOI: 10.1016/j.aca.2023.342072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. RESULTS We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 min without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. SIGNIFICANCE IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA; Department of Public Health, Purdue University, West Lafayette, IN, USA.
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4
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Li H, Ding L, Liao R, Li N, Hong X, Jiang Z, Liu D. Global genomic diversity and conservation of SARS-CoV-2 since the COVID-19 outbreak. Microbiol Spectr 2023; 11:e0282623. [PMID: 37909759 PMCID: PMC10714991 DOI: 10.1128/spectrum.02826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Our results indicate that most severe acute respiratory syndrome coronavirus 2 genomes sampled from patients had a mutation rate ≤1.07 ‰ and genome-tail proteins (including S protein) were the main sources of genetic polymorphism. The analysis of the virus-host interaction network of genome-tail proteins showed that they shared some antiviral signaling pathways, especially the intracellular protein transport pathway.
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Affiliation(s)
- Heng Li
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
- Department of Geriatrics, Geriatric Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Liping Ding
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Rui Liao
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Nini Li
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiaoping Hong
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
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5
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Arabi-Jeshvaghani F, Javadi-Zarnaghi F, Löchel HF, Martin R, Heider D. LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens. Infection 2023; 51:1809-1818. [PMID: 37828369 DOI: 10.1007/s15010-023-02100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE AND METHODS The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation. RESULTS LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database. CONCLUSION LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.
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Affiliation(s)
- Fatemeh Arabi-Jeshvaghani
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Hannah Franziska Löchel
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Roman Martin
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Dominik Heider
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an Integrated Sample Amplification Control for Salivary Point-of-Care Pathogen Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296477. [PMID: 37873363 PMCID: PMC10593008 DOI: 10.1101/2023.10.03.23296477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. Results We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 minutes without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. Significance IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F. K. Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C. Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Department of Public Health, Purdue University, West Lafayette, IN, USA
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7
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Hongjaisee S, Kham-Kjing N, Musikul P, Daengkaokhew W, Kongson N, Guntala R, Jaiyapan N, Kline E, Panpradist N, Ngo-Giang-Huong N, Khamduang W. A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA. Diagnostics (Basel) 2023; 13:3040. [PMID: 37835783 PMCID: PMC10572433 DOI: 10.3390/diagnostics13193040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65 °C for 30 min using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand;
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
| | - Nang Kham-Kjing
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Piyagorn Musikul
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Wannaporn Daengkaokhew
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Nuntita Kongson
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | | | - Nitipoom Jaiyapan
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Enos Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
| | - Nuttada Panpradist
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Nicole Ngo-Giang-Huong
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Agropolis University Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Pour le Développement (IRD), 34394 Montpellier, France
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
| | - Woottichai Khamduang
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
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Yaren O, McCarter J, Morris AR, Bradley KM, Karalkar NB, McLendon DC, Kim D, Eastmond BH, Burkett-Cadena ND, Alto BW, Benner SA. Multiplex Surveillance Kit Using Sweetened Solid Support to Detect Arboviruses Isothermally in Mosquito Saliva from the Field. Anal Chem 2023; 95:10736-10743. [PMID: 37390024 DOI: 10.1021/acs.analchem.3c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Recently reported "displaceable probe" loop amplification (DP-LAMP) architecture has shown to amplify viral RNA from SARS-CoV-2 with little sample processing. The architecture allows signals indicating the presence of target nucleic acids to be spatially separated, and independent in sequence, from the complicated concatemer that LAMP processes create as part of their amplification process. This makes DP-LAMP an attractive molecular strategy to integrate with trap and sampling innovations to detect RNA from arboviruses carried by mosquitoes in the field. These innovations include (a) development of organically produced carbon dioxide with ethylene carbonate as a bait deployable in mosquito trap, avoiding the need for dry ice, propane tanks, or inorganic carbonates and (b) a process that induces mosquitoes to lay virus-infected saliva on a quaternary ammonium-functionalized paper (Q-paper) matrix, where (c) the matrix (i) inactivates the deposited viruses, (ii) releases their RNA, and (iii) captures viral RNA in a form that keeps it stable for days at ambient temperatures. We report this integration here, with a surprisingly simple workflow. DP-LAMP with a reverse transcriptase was found to amplify arboviral RNA directly from Q-paper, without requiring a separate elution step. This capture-amplification-detection architecture can be multiplexed, with the entire system integrated into a device that can support a campaign of surveillance, in the wild outdoors, that reports the prevalence of arboviruses from field-captured mosquitoes.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Jacquelyn McCarter
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Andrew R Morris
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- College of Medicine, University of Florida, Gainesville, Florida 32611,, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Nilesh B Karalkar
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Daniel C McLendon
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Dongmin Kim
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Bradley H Eastmond
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
- Thermo Fisher Scientific, Frederick, Maryland 02451, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
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9
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Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
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Affiliation(s)
- Adrián Szobi
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Halil Önder Özbaşak
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Sandra Szeibeczederová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Liudmyla Kapustian
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Zuzana Hudáčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- Stanford University, 730 Escondido Rd., Stanford, CA, 94305, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- University of Cologne, Institute for Biological Physics, Zülpicher Str. 77, 50937, Köln, Germany
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Piotr Putaj
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Stanislava Bírová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Ivana Čirková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Martin Čarnecký
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Kilián
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Jurkáček
- AstonITM s.r.o., Račianska 153, 831 54, Bratislava, Slovakia
| | - Viktória Čabanová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Kristína Boršová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Veronika Vaňová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
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10
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Hoffman JS, Hirano M, Panpradist N, Breda J, Ruth P, Xu Y, Lester J, Nguyen BH, Ceze L, Patel SN. Passively sensing SARS-CoV-2 RNA in public transit buses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:152790. [PMID: 35007574 PMCID: PMC8741327 DOI: 10.1016/j.scitotenv.2021.152790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/24/2021] [Accepted: 12/26/2021] [Indexed: 05/25/2023]
Abstract
Affordably tracking the transmission of respiratory infectious diseases in urban transport infrastructures can inform individuals about potential exposure to diseases and guide public policymakers to prepare timely responses based on geographical transmission in different areas in the city. Towards that end, we designed and tested a method to detect SARS-CoV-2 RNA in the air filters of public buses, revealing that air filters could be used as passive fabric sensors for the detection of viral presence. We placed and retrieved filters in the existing HVAC systems of public buses to test for the presence of trapped SARS-CoV-2 RNA using phenol-chloroform extraction and RT-qPCR. SARS-CoV-2 RNA was detected in 14% (5/37) of public bus filters tested in Seattle, Washington, from August 2020 to March 2021. These results indicate that this sensing system is feasible and that, if scaled, this method could provide a unique lens into the geographically relevant transmission of SARS-CoV-2 through public transit rider vectors, pooling samples of riders over time in a passive manner without installing any additional systems on transit vehicles.
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Affiliation(s)
- Jason S Hoffman
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA.
| | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, 185 Stevens Way, Seattle 98195, WA, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle 98105, WA, USA
| | - Joseph Breda
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA
| | - Parker Ruth
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA; Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle 98105, WA, USA
| | - Yuanyi Xu
- Department of Microbiology, University of Washington, 1705 NE Pacific St, Seattle 98195, WA, USA; Department of Chemistry, University of Washington, 4000 15th Ave NE, Seattle 98195, WA, USA
| | - Jonathan Lester
- Microsoft Research, 14820 NE 36th St, Redmond 98052, WA, USA
| | | | - Luis Ceze
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA
| | - Shwetak N Patel
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA; Department of Electrical and Computer Engineering, University of Washington, 185 Stevens Way, Seattle 98195, WA, USA
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11
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Panpradist N, Kline EC, Atkinson RG, Roller M, Wang Q, Hull IT, Kotnik JH, Oreskovic AK, Bennett C, Leon D, Lyon V, Gilligan-Steinberg SD, Han PD, Drain PK, Starita LM, Thompson MJ, Lutz BR. Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection. SCIENCE ADVANCES 2021; 7:eabj1281. [PMID: 34910507 PMCID: PMC8673764 DOI: 10.1126/sciadv.abj1281] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/26/2021] [Indexed: 05/22/2023]
Abstract
RNA amplification tests sensitively detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but their complexity and cost are prohibitive for expanding coronavirus disease 2019 (COVID-19) testing. We developed “Harmony COVID-19,” a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device. Our ready-to-use, multiplexed reverse transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μl and can report in 17 min for high–viral load samples (5000 copies/μl). Harmony detected 97 or 83% of contrived samples with ≥0.5 viral particles/μl in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens (n = 101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μl, with 100% specificity in specimens positive for other respiratory pathogens. Extraction-free analysis (n = 29) had 95% success in specimens with ≥1 RNA copies/μl. Usability testing performed first time by health care workers showed 95% accuracy.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Global Health for Women, Adolescents, and Children, School of Public Health, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Robert G. Atkinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Michael Roller
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jack H. Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Crissa Bennett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Daniel Leon
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Victoria Lyon
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | | | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul K. Drain
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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